[gmx-users] umbrella sampling tutorial

[Ming Tang]

Dear Justin,

The results turned out that the COM distance between them is the same over time, seems that both Chain_A and Chain_B had been pulled by the same force in the same direction, which is different from the tutorial.



From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Ming Tang
Sent: Thursday, 12 March 2015 11:34 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial

Hi Justin,

Your code works!
Thank you very much.

Regards,
Ming

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Thursday, 12 March 2015 11:18 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/11/15 8:58 PM, Ming Tang wrote:
> Dear Justin,
>
> Thanks for your help.
> I changed the group names to Chain_A and Chain_B in my index file, and modified the COM pulling code.
>
> ; COM pulling
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull-ngroups    = 1
> ?assign the reference group?
> pull-group1-name    = Chain_A
> pull-coord1-rate      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2
>
> But I didn't found the order to assign the reference group Chain_B in 
> GROMACS 5.0.4 Could you give me some help?
>

Something like this (I haven't tested it, so please let me know if this works...or doesn't):

pull                = umbrella
pull-geometry       = distance
pull-dim            = N N Y
pull-start          = yes
pull-ngroups        = 2
pull-ncoords        = 1
pull-coord1-groups  = 1 2
pull-group1-name    = Chain_A
pull-group2-name    = Chain_B
pull-coord1-rate    = 0.01
pull-coord1-k       = 1000

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

==================================================
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.